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- PDB-3dyh: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphospho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dyh | ||||||
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Title | T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-721 | ||||||
![]() | Farnesyl pyrophosphate synthase![]() | ||||||
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Function / homology | ![]() transferase activity, transferring alkyl or aryl (other than methyl) groups / isoprenoid biosynthetic process / ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cao, R. / Gao, Y. / Robinson, H. / Goddard, A. / Oldfield, E. | ||||||
![]() | ![]() Title: Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation. Authors: Zhang, Y. / Cao, R. / Yin, F. / Hudock, M.P. / Guo, R.T. / Krysiak, K. / Mukherjee, S. / Gao, Y.G. / Robinson, H. / Song, Y. / No, J.H. / Bergan, K. / Leon, A. / Cass, L. / Goddard, A. / ...Authors: Zhang, Y. / Cao, R. / Yin, F. / Hudock, M.P. / Guo, R.T. / Krysiak, K. / Mukherjee, S. / Gao, Y.G. / Robinson, H. / Song, Y. / No, J.H. / Bergan, K. / Leon, A. / Cass, L. / Goddard, A. / Chang, T.K. / Lin, F.Y. / Van Beek, E. / Papapoulos, S. / Wang, A.H. / Kubo, T. / Ochi, M. / Mukkamala, D. / Oldfield, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.3 KB | Display | ![]() |
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PDB format | ![]() | 128 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2opmC ![]() 2zeuC ![]() 2zevC ![]() 3dyfC ![]() 3dygC ![]() 3efqC ![]() 3egtC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 44475.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q86C09, (2E,6E)-farnesyl diphosphate synthase #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.81 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.75 Details: 10% MPD, 0.1 AMMONIUM ACETATE, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 123.2 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2008 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.94→30 Å / Num. obs: 65909 / % possible obs: 98.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.94→2.02 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.509 / % possible all: 89.1 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.964 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→28.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.992 Å / Total num. of bins used: 20
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